Course content

The course is mostly aimed at researchers getting into their first de novo genome assembly project, but will also include information of use for the more experienced researcher. We will cover assembly of both prokaryotes and eukaryotes (see our sister course in metagenomics for assembly of mixed/environmental samples) and spend a lot of time on learning how to run the analyses in hands-on computer exercises. Applicants will be taken through all steps of a genome assembly project, from the quality assessment of data, through assembly, to validation of assemblies. After this course, the students will be well aware of common practices in genome assembly projects and will know how to avoid common pitfalls.

Topics covered will include:

Different sequencing technologies and their use in genome assembly, including Illumina and PacBio data

Quality assessment of data

Quality based cleaning and adapter trimming

Assembly of genomes including overview of commonly used programs

Assembly validation

Contamination analyses

Entry requirements

This is an advanced course. Participants must be comfortable navigating a linux shell and executing programs from the command line. Without this knowledge, it will be impossible to participate in the computer exercises. Previous experience from working with NGS data (e.g., transcriptome assembly, SNP calling) is a plus. Applicants are encouraged to bring their own laptops, but there will be computers to use for participants unable to do so.

Due to space constraints for the computer exercises, there is a maximum number of allowed participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.

Date and time

2017-11-15 - 2017-11-17

Location

Husargatan 3, Uppsala

SciLifeLab has been created by the coordinated effort of four universities in Stockholm and Uppsala: Stockholm University, Karolinska Institutet, KTH Royal Institute of Technology and Uppsala University.